Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	CP009273	2,400,257	IS5 (+) +4 bp	intergenic (‑137/‑780)	lrhA ← / → alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	2282398 =	NA (NA)	42 (0.600)	37/296	1.3	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	CP009273	2400257 =	0 (0.000)					intergenic (‑137/‑783)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
*	?	CP009273	= 2283592	NA (NA)	73 (1.040)	57/296	0.2	100%	noncoding (1/1195 nt)	IS5	repeat region
	?	CP009273	= 2400260	0 (0.000)					intergenic (‑140/‑780)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

ATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/2282522‑2282398 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGT  >  CP009273/2400257‑2400402                                                                                                                                                                                                                                                                                  gTGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCGCAAACATGAAGAAATGAACTGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTC                                                                                                                            <  1:658934/148‑1      GAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGACTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTA                                                                                                                       >  1:291042/1‑149       AAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTAT                                                                                                                      >  2:540899/1‑149         GAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAA                                                                                                                    <  1:1081541/149‑1           AACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATG                                                                                                                  <  1:116462/149‑1               GTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGACTCAAACATGGAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTCTAATGCCTG                                                                                                              >  1:756607/1‑149                  TAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAACAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAG                                                                                                           >  1:292907/1‑149                  TAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAG                                                                                                           >  1:292280/1‑149                   AAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGT                                                                                                          <  1:38221/149‑1                         GCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCACAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGCTATAATGCCTGAAGTAGATCc                                                                                                    >  1:715209/1‑148                          CTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAATTAGATCAC                                                                                                   >  2:576787/1‑149                                             cGAGAAAAAATCGTCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGAT                                                                                <  1:506231/148‑1                                             GGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGAT                                                                                >  2:326304/1‑149                                               AGAAAAAATCTGCTCAAACATGAAGAAATGAAATGACGGAGTCAGCCGAGAAGAATTTCCCCGCTTATCCGCCCCTT‑CACTAAATAAGCGAGTCTCATCGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCG                                                                              <  2:962426/149‑1                                                      ATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCT                                                                       <  2:74933/149‑1                                                          GCTCAAACATGAAGAAATGAAATGACTGAGCCAGCCGAGAAGAATTCCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTA                                                                   <  2:723568/149‑1                                                            TCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTG‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTAAGGGATAGCATATCTATTAAG                                                                 >  2:743631/1‑149                                                             CAAACATGAAGAAATGAAATGACTGGGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTGATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGT                                                                <  2:1015875/149‑1                                                              AAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCGATTAAGTT                                                               >  1:430751/1‑149                                                               AACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCATATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAACGATCGCATATCTATTAAGTTA                                                              >  1:290040/1‑149                                                                 CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGCACTTCCACCCTT‑TTTGGACCTTAACCTAAAAGAGCGACTCACATCGTGCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACT                                                            <  1:1095111/149‑1                                                                  ATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTC                                                           >  2:730998/1‑149                                                                      AGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTC                                                       <  2:609742/149‑1                                                                        AAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTTTTCCGTTATAATGCCTGAAGTAGATCACAGACTATATCTTCAGTGATCGCATCTCGATTACGTTACTCACCCTT                                                     >  1:73300/1‑149                                                                        AAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTT                                                     >  2:17590/1‑149                                                                          agGAAATGACTGGGTCAGCCGAGAAGAACTTCCCCGCTTATCCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGCTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTT                                                   <  2:406151/147‑1                                                                             AAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTA                                                >  2:1075770/1‑149                                                                              AATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTAT                                               >  2:490809/1‑149                                                                              AATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTATTTTCTAT                                               >  2:898154/1‑149                                                                                TGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAACCGACTCACAACGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTCAGTTACTCCCTCTTTTCTATTT                                             >  2:572997/1‑149                                                                                    tggGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTC‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGACGTAGATCACAGCATATATCTTCAGGGATCCAATCTCTATTAAGTTACTCAATCTTTTCTATTTATGA                                         <  1:293202/146‑1                                                                                       GTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATATATTAAGTTACTCACTCTTTTCTATTTATGACAT                                      >  2:599760/1‑149                                                                                                 agGAATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTT                            <  2:442678/147‑1                                                                                                 AAGAATTTCCCCGCTTATTCTCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTT                            <  1:625349/149‑1                                                                                                     ATTTCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAT                        <  1:1014063/149‑1                                                                                                        cCCCCGCTTATCCGCACCTT‑CCCTAAAAAAGCGCCTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATAGCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAA                     <  2:191588/148‑1                                                                                                        TCCCCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAA                     <  2:1082453/149‑1                                                                                                           CCGCTTATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGT                  >  2:62900/1‑149                                                                                                                 ATTCGCACCTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGT            <  1:1010459/149‑1                                                                                                                   TCGCACCTT‑CCCTAAAACAGCGACTCTCATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGTGTGTTTGTATAAATGTAAATGTGA          <  1:1008176/149‑1                                                                                                                         CTT‑CCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTT    <  2:265652/149‑1                                                                                                                           T‑CCCTAAAAAAGCGACTCACATTGTTCCTTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGT  >  2:615186/1‑149                                                                                                                                                                                                                                                                                  ATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTT‑CC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/2282522‑2282398 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGT  >  CP009273/2400257‑2400402

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.